StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline.

ABSTRACT: Label-free quantification has grown in popularity as a means of obtaining relative abundance measures for proteomics experiments. However, easily accessible and integrated tools to perform label-free quantification have been lacking. We describe StPeter, an implementation of Normalized Spectral Index quantification for wide availability through integration into the widely used Trans-Proteomic Pipeline. This implementation has been specifically designed for reproducibility and ease of use. We demonstrate that StPeter outperforms other state-of-the art packages using a recently reported benchmark data set over the range of false discovery rates relevant to shotgun proteomics results. We also demonstrate that the software is computationally efficient and supports data from a variety of instru

SUBMITTER: Hoopmann MR 

PROVIDER: S-EPMC5891225 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature